A large alpine meadow in a seasonal permafrost zone exists in the west of Sichuan, which belongs to a part of the Qinghai–Tibet Plateau, China. Due to the extreme climates and repeated freeze–thaw cycling, resulting in a diminishment in soil shear strength, disasters occur frequently. Plant roots increase the complexity of the soil freeze–thaw strength problem. This study applied the freeze–thaw cycle and direct shear tests to investigate the change in the shear strength of root-soil composite under freeze–thaw cycles. This study examined how freeze–thaw cycles and initial moisture content affect the shear strength of two sorts of soil: uncovered soil and root-soil composite. By analyzing the test information, the analysts created numerical conditions to foresee the shear quality of both sorts of soil under shifting freeze–thaw times and starting moisture levels. The results showed that: (1) Compared to the bare soil, the root-soil composite was less affected by freeze–thaw cycles in the early stage, and the shear strength of both sorts of soil was stabilized after 3–5 freeze–thaw cycles. (2) The cohesion of bare soil decreased more than that of root-soil composite with increasing moisture content. However, freeze–thaw cycles primarily influence soil cohesion more than the internal friction angle. The cohesion modification leads to changes in shear quality for both uncovered soil and root-soil composite. (3) The fitting equations obtained via experiments were used to simulate direct shear tests. The numerical results are compared with the experimental data. The difference in the soil cohesion and root-soil composite cohesion between the experiment data and the simulated result is 8.2% and 17.2%, respectively, which indicates the feasibility of the fitting equations applied to the numerical simulation of the soil and root-soil composite under the freeze–thaw process. The findings give potential applications on engineering and disaster prevention in alpine regions.